# Date 2008-01-16 Time 01:22:20 PST -0800 (1200475340.06 s)
#phil __OFF__

Command line arguments: "../395.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21098
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 395

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.2261, 88.5498, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.9724
Completeness in resolution range: 0.945963
Completeness with d_max=infinity: 0.943094

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9810
                             d_min =   1.9724

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.981 1.9724
Completeness in resolution range: 0.945963
Completeness with d_max=infinity: 0.943094

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9814 -  4.2207 [2176/2200]  1956   220  10.1%
  bin  2:  4.2207 -  3.3626 [2089/2109]  1881   208  10.0%
  bin  3:  3.3626 -  2.9412 [2064/2083]  1861   203   9.8%
  bin  4:  2.9412 -  2.6739 [2032/2062]  1822   210  10.3%
  bin  5:  2.6739 -  2.4832 [2034/2053]  1833   201   9.9%
  bin  6:  2.4832 -  2.3374 [2033/2058]  1827   206  10.1%
  bin  7:  2.3374 -  2.2207 [1997/2025]  1802   195   9.8%
  bin  8:  2.2207 -  2.1243 [2001/2037]  1800   201  10.0%
  bin  9:  2.1243 -  2.0427 [1991/2039]  1796   195   9.8%
  bin 10:  2.0427 -  1.9724 [1172/2042]  1052   120  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_395/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: 0.15 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:
        1.11 -     1.87: 11
        1.87 -     2.63: 75
        2.63 -     3.38: 4286
        3.38 -     4.14: 9380
        4.14 -     4.90: 14640
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.111 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.504 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.524 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  53 " - " O   HOH Z 102 "  1.680 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 104 "  1.723 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28387 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_395/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_395/model_refine_001.geo

CPU time processing inputs: 9.52


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.22605 88.54975 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5029   r_free= 0.4903   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.300084                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7077 0.99   1412  154 0.4177 0.4031      6.6318      6.5953|
|  2:  4.7077 -  3.7560 0.99   1359  154 0.4305 0.4354      6.8184      6.8566|
|  3:  3.7560 -  3.2869 0.99   1326  149 0.4694 0.4196      6.7119      6.6873|
|  4:  3.2869 -  2.9890 0.99   1335  147 0.5072 0.4869      6.5645      6.5084|
|  5:  2.9890 -  2.7762 0.99   1303  146 0.5348 0.4776      6.3804      6.4202|
|  6:  2.7762 -  2.6135 0.99   1315  147 0.5325 0.5635      6.3003      6.2233|
|  7:  2.6135 -  2.4832 0.99   1303  145 0.5391 0.5013      6.2487       6.167|
|  8:  2.4832 -  2.3755 0.98   1302  141 0.5566 0.5233      6.2006      6.2189|
|  9:  2.3755 -  2.2844 0.98   1290  143 0.5283 0.5601      6.1186       6.203|
| 10:  2.2844 -  2.2058 1.00   1299  144 0.5544 0.5437      6.1166      6.0971|
| 11:  2.2058 -  2.1371 0.98   1273  148 0.5325 0.5233      6.0282      6.0517|
| 12:  2.1371 -  2.0761 0.98   1299  137 0.5403 0.5268      5.9743      5.9867|
| 13:  2.0761 -  2.0216 0.93   1222  135 0.5376 0.5008       5.887      5.8314|
| 14:  2.0216 -  1.9724 0.46    592   69 0.5367 0.5293      5.9055       5.805|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7077  1412   154  0.67  37.23   0.78     0.72      84138.38|
|  2:  4.7077 -  3.7560  1359   154  0.67  37.91   0.86     0.75     121201.93|
|  3:  3.7560 -  3.2869  1326   149  0.56  47.34   0.82     0.69     127694.23|
|  4:  3.2869 -  2.9890  1335   147  0.43  57.10   0.76     0.53     118463.27|
|  5:  2.9890 -  2.7762  1303   146  0.30  67.53   0.72     0.37      96648.42|
|  6:  2.7762 -  2.6135  1315   147  0.22  73.50   0.70     0.26      88317.20|
|  7:  2.6135 -  2.4832  1303   145  0.19  76.03   0.71     0.22      78029.33|
|  8:  2.4832 -  2.3755  1302   141  0.21  74.25   0.70     0.26      69758.56|
|  9:  2.3755 -  2.2844  1290   143  0.24  72.34   0.73     0.28      62454.10|
| 10:  2.2844 -  2.2058  1299   144  0.25  71.28   0.72     0.30      54460.30|
| 11:  2.2058 -  2.1371  1273   148  0.22  73.33   0.75     0.29      53492.77|
| 12:  2.1371 -  2.0761  1299   137  0.23  72.68   0.74     0.30      47548.31|
| 13:  2.0761 -  2.0216  1222   135  0.25  71.40   0.71     0.32      40969.29|
| 14:  2.0216 -  1.9724   592    69  0.32  65.85   0.75     0.36      31447.48|
|alpha:            min =        0.22 max =            0.75 mean =         0.41|
|beta:             min =    31447.48 max =       127694.23 mean =     79149.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.72|
|phase err.(test): min =        0.00 max =           89.99 mean =        63.97|
|-----------------------------------------------------------------------------|

============================== 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 = 20.153828             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.140   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.112723              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.103   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.138 -  1.514:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.514 -  1.890:       19 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.890 -  2.266:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.266 -  2.643:      626 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.643 -  3.019:     1464 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.019 -  3.395:     2554 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.395 -  3.771:     3956 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.771 -  4.148:     5140 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.148 -  4.524:     6652 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.524 -  4.900:     7798 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.672 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.138 |       2.179 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.773)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    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:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.773)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5085   r_free= 0.4943   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.301103                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4941   r_free= 0.4786   ksol= 0.37   Bsol= 20.00   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.64,7.85,10.73,0.00,0.00,0.00); trace/3= 8.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.293841                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.093205             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.847   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.672908              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.890   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4941      final r-factor (work) = 0.4279          |
| start r-factor (free) = 0.4786      final r-factor (free) = 0.4492          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.3189 = 16.09 * 0.50 * 6.2942 + 1.00 * 53.6718                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.3599 = 16.09 * 0.50 * 6.2402 + 1.00 * 0.1474                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4279      final r-factor (work) = 0.3874          |
| start r-factor (free) = 0.4492      final r-factor (free) = 0.4479          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4538 = 1.67 * 1.00 * 6.2402 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.3563 = 1.67 * 1.00 * 6.1779 + 1.00 * 0.0212                              |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.773)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.02   15.47    None  None   None       |
|    all(noH): 2823   0      0.00    78.02   15.47    None  None   None       |
|    Sol.    : 438    0      0.00    78.02   24.51    None  None   None       |
|    Mac.    : 2385   0      0.00    69.75   13.81    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 -   7.802:  880   |   5:    39.011 -  46.813:   81        |
|      1:     7.802 -  15.604:  769   |   6:    46.813 -  54.615:   43        |
|      2:    15.604 -  23.406:  541   |   7:    54.615 -  62.417:   19        |
|      3:    23.406 -  31.208:  334   |   8:    62.417 -  70.219:    7        |
|      4:    31.208 -  39.011:  148   |   9:    70.219 -  78.021:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3874 r_free = 0.4479             target_work(ml) = 6.168         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3870 r_free = 0.4479             target_work(ml) = 6.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3870   r_free= 0.4479   ksol= 0.37   Bsol= 20.00   scale= 1.108   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.64,7.85,10.73,0.00,0.00,0.00); trace/3= 8.07                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.166954                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3857   r_free= 0.4455   ksol= 0.35   Bsol= 39.13   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,4.39,7.44,0.00,0.00,0.00); trace/3= 4.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.169127                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.723677              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.189  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.700943              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.397  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3857      final r-factor (work) = 0.3201          |
| start r-factor (free) = 0.4455      final r-factor (free) = 0.3890          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9902 = 7.72 * 0.50 * 6.1739 + 1.00 * 0.1474                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6277 = 7.72 * 0.50 * 6.0951 + 1.00 * 0.0894                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3201      final r-factor (work) = 0.3001          |
| start r-factor (free) = 0.3890      final r-factor (free) = 0.3717          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2934 = 0.70 * 1.00 * 6.0951 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2233 = 0.70 * 1.00 * 6.0064 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.773)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.48   14.82    None  None   None       |
|    all(noH): 2823   0      0.00    88.48   14.82    None  None   None       |
|    Sol.    : 438    0      0.00    88.48   29.70    None  None   None       |
|    Mac.    : 2385   0      0.00    64.34   12.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.848: 1117   |   5:    44.241 -  53.089:   53        |
|      1:     8.848 -  17.696:  827   |   6:    53.089 -  61.938:   23        |
|      2:    17.696 -  26.545:  469   |   7:    61.938 -  70.786:   11        |
|      3:    26.545 -  35.393:  212   |   8:    70.786 -  79.634:    6        |
|      4:    35.393 -  44.241:  104   |   9:    79.634 -  88.482:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3001 r_free = 0.3717             target_work(ml) = 5.988         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2999 r_free = 0.3723             target_work(ml) = 5.988         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2999   r_free= 0.3723   ksol= 0.35   Bsol= 39.13   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,4.39,7.44,0.00,0.00,0.00); trace/3= 4.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.988468                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2994   r_free= 0.3720   ksol= 0.34   Bsol= 57.25   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.62,2.53,5.20,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 5.988959                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.781142              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.692  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.451639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.603  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2994      final r-factor (work) = 0.2204          |
| start r-factor (free) = 0.3720      final r-factor (free) = 0.2849          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.4594 = 7.78 * 0.50 * 6.0068 + 1.00 * 0.0894                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9592 = 7.78 * 0.50 * 5.8775 + 1.00 * 0.0923                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2204      final r-factor (work) = 0.1953          |
| start r-factor (free) = 0.2849      final r-factor (free) = 0.2584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6679 = 0.45 * 1.00 * 5.8775 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5798 = 0.45 * 1.00 * 5.6778 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.773)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.65  14.29    None  None   None       |
|    all(noH): 2823   0      0.00    112.65  14.29    None  None   None       |
|    Sol.    : 438    0      1.46    89.09   35.07    None  None   None       |
|    Mac.    : 2385   0      0.00    112.65  10.47    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 -  11.266: 1618   |   5:    56.328 -  67.593:   21        |
|      1:    11.266 -  22.531:  665   |   6:    67.593 -  78.859:   10        |
|      2:    22.531 -  33.797:  229   |   7:    78.859 -  90.124:    1        |
|      3:    33.797 -  45.062:  192   |   8:    90.124 - 101.390:    0        |
|      4:    45.062 -  56.328:   86   |   9:   101.390 - 112.655:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1953 r_free = 0.2584             target_work(ml) = 5.627         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1950 r_free = 0.2578             target_work(ml) = 5.626         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1950   r_free= 0.2578   ksol= 0.34   Bsol= 57.25   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.62,2.53,5.20,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.625566                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1941   r_free= 0.2574   ksol= 0.32   Bsol= 57.25   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.56,1.22,3.53,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.627089                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.847977              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.168  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.477984              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.107  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1941      final r-factor (work) = 0.1534          |
| start r-factor (free) = 0.2574      final r-factor (free) = 0.2107          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8696 = 4.85 * 0.50 * 5.6837 + 1.00 * 0.0924                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4923 = 4.85 * 0.50 * 5.5357 + 1.00 * 0.0740                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1534      final r-factor (work) = 0.1416          |
| start r-factor (free) = 0.2107      final r-factor (free) = 0.2001          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7514 = 2.48 * 1.00 * 5.5357 + 1.00 * 0.0341                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.3633 = 2.48 * 1.00 * 5.3865 + 1.00 * 0.0157                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.773)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.45  15.40    None  None   None       |
|    all(noH): 2823   0      0.00    100.45  15.40    None  None   None       |
|    Sol.    : 438    0      2.83    100.45  43.36    None  None   None       |
|    Mac.    : 2385   0      0.00    92.49   10.26    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.045: 1574   |   5:    50.224 -  60.269:   93        |
|      1:    10.045 -  20.090:  655   |   6:    60.269 -  70.314:   61        |
|      2:    20.090 -  30.134:  183   |   7:    70.314 -  80.359:   33        |
|      3:    30.134 -  40.179:  102   |   8:    80.359 -  90.403:    9        |
|      4:    40.179 -  50.224:  107   |   9:    90.403 - 100.448:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1416 r_free = 0.2001             target_work(ml) = 5.357         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1415 r_free = 0.1999             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1999   ksol= 0.32   Bsol= 57.25   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.56,1.22,3.53,0.00,0.00,0.00); trace/3= 1.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.355628                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1417   r_free= 0.2001   ksol= 0.33   Bsol= 62.67   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.40,0.82,3.10,0.00,0.00,0.00); trace/3= 1.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.354824                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.487969              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.082  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.223531              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.536  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1417      final r-factor (work) = 0.1295          |
| start r-factor (free) = 0.2001      final r-factor (free) = 0.1829          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7757 = 2.49 * 0.50 * 5.3872 + 1.00 * 0.0741                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6823 = 2.49 * 0.50 * 5.3229 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1295      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1829      final r-factor (free) = 0.1763          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2054 = 0.22 * 1.00 * 5.3229 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1914 = 0.22 * 1.00 * 5.2810 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.773)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.72   14.48    None  None   None       |
|    all(noH): 2823   0      0.00    94.72   14.48    None  None   None       |
|    Sol.    : 438    0      3.18    94.72   40.01    None  None   None       |
|    Mac.    : 2385   0      0.00    93.64   9.79     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 -   9.472: 1574   |   5:    47.362 -  56.834:   78        |
|      1:     9.472 -  18.945:  687   |   6:    56.834 -  66.306:   59        |
|      2:    18.945 -  28.417:  163   |   7:    66.306 -  75.778:   29        |
|      3:    28.417 -  37.889:  119   |   8:    75.778 -  85.251:    8        |
|      4:    37.889 -  47.362:   98   |   9:    85.251 -  94.723:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1763             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1281 r_free = 0.1761             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1761   ksol= 0.33   Bsol= 62.67   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.40,0.82,3.10,0.00,0.00,0.00); trace/3= 1.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.260434                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7077 0.99   1412  154 0.1019 0.1333      5.4392      5.5995|
|  2:  4.7077 -  3.7560 0.99   1359  154 0.0933 0.1303       5.539      5.7701|
|  3:  3.7560 -  3.2869 0.99   1326  149 0.1222 0.1691      5.6084      5.9353|
|  4:  3.2869 -  2.9890 0.99   1335  147 0.1438 0.1982      5.5915      5.7834|
|  5:  2.9890 -  2.7762 0.99   1303  146 0.1544 0.1765      5.4679      5.6037|
|  6:  2.7762 -  2.6135 0.99   1315  147 0.1407 0.2379      5.3237      5.6301|
|  7:  2.6135 -  2.4832 0.99   1303  145 0.1513 0.1834      5.3048      5.4203|
|  8:  2.4832 -  2.3755 0.98   1302  141 0.1431 0.1922      5.2285      5.4483|
|  9:  2.3755 -  2.2844 0.98   1290  143 0.1413 0.2064      5.1573      5.4465|
| 10:  2.2844 -  2.2058 1.00   1299  144 0.1312 0.1793        5.08      5.2567|
| 11:  2.2058 -  2.1371 0.98   1273  148 0.1326 0.1967      5.0305      5.3421|
| 12:  2.1371 -  2.0761 0.98   1299  137 0.1357 0.1915       4.995      5.3056|
| 13:  2.0761 -  2.0216 0.93   1222  135 0.1181 0.1701      4.8187      4.9847|
| 14:  2.0216 -  1.9724 0.46    592   69 0.1007 0.1540      4.6527      4.9129|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7077  1412   154  0.93  10.57   0.97     0.94       8662.99|
|  2:  4.7077 -  3.7560  1359   154  0.94   9.53   1.02     0.99      11267.85|
|  3:  3.7560 -  3.2869  1326   149  0.91  13.89   1.03     1.02      13686.80|
|  4:  3.2869 -  2.9890  1335   147  0.90  16.33   1.02     1.01      13542.93|
|  5:  2.9890 -  2.7762  1303   146  0.88  18.60   1.00     0.97      11111.77|
|  6:  2.7762 -  2.6135  1315   147  0.88  18.37   0.98     0.94       8669.21|
|  7:  2.6135 -  2.4832  1303   145  0.88  18.45   1.00     0.97       7943.79|
|  8:  2.4832 -  2.3755  1302   141  0.88  18.37   1.00     0.97       7169.69|
|  9:  2.3755 -  2.2844  1290   143  0.89  17.96   1.01     0.96       6316.75|
| 10:  2.2844 -  2.2058  1299   144  0.88  18.00   1.01     0.96       5470.44|
| 11:  2.2058 -  2.1371  1273   148  0.88  18.40   1.00     0.96       5273.41|
| 12:  2.1371 -  2.0761  1299   137  0.89  18.01   1.01     1.00       4838.95|
| 13:  2.0761 -  2.0216  1222   135  0.90  16.90   1.00     0.99       3553.90|
| 14:  2.0216 -  1.9724   592    69  0.94  12.28   0.99     0.97       2333.59|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2333.59 max =        13686.80 mean =      8129.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        16.21|
|phase err.(test): min =        0.00 max =           89.50 mean =        15.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1761   ksol= 0.33   Bsol= 64.01   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-0.63,1.60,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.260332                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1761   ksol= 0.33   Bsol= 64.01   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.97,-0.63,1.60,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.260332                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9814 -  4.7077 0.99   1412  154 0.1019 0.1333       5.439      5.5976|
|  2:  4.7077 -  3.7560 0.99   1359  154 0.0932 0.1302       5.538      5.7693|
|  3:  3.7560 -  3.2869 0.99   1326  149 0.1222 0.1691      5.6084      5.9357|
|  4:  3.2869 -  2.9890 0.99   1335  147 0.1438 0.1983      5.5916      5.7837|
|  5:  2.9890 -  2.7762 0.99   1303  146 0.1544 0.1764       5.468       5.604|
|  6:  2.7762 -  2.6135 0.99   1315  147 0.1408 0.2379      5.3239      5.6303|
|  7:  2.6135 -  2.4832 0.99   1303  145 0.1512 0.1836      5.3048      5.4206|
|  8:  2.4832 -  2.3755 0.98   1302  141 0.1431 0.1923      5.2287       5.449|
|  9:  2.3755 -  2.2844 0.98   1290  143 0.1413 0.2065      5.1574      5.4468|
| 10:  2.2844 -  2.2058 1.00   1299  144 0.1312 0.1795        5.08      5.2571|
| 11:  2.2058 -  2.1371 0.98   1273  148 0.1325 0.1963      5.0303      5.3411|
| 12:  2.1371 -  2.0761 0.98   1299  137 0.1357 0.1915      4.9951      5.3061|
| 13:  2.0761 -  2.0216 0.93   1222  135 0.1181 0.1700      4.8184      4.9846|
| 14:  2.0216 -  1.9724 0.46    592   69 0.1007 0.1537      4.6522      4.9115|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9814 -  4.7077  1412   154  0.93  10.54   0.97     0.94       8632.87|
|  2:  4.7077 -  3.7560  1359   154  0.94   9.51   1.01     0.99      11239.28|
|  3:  3.7560 -  3.2869  1326   149  0.91  13.89   1.03     1.02      13684.62|
|  4:  3.2869 -  2.9890  1335   147  0.90  16.33   1.01     1.01      13544.61|
|  5:  2.9890 -  2.7762  1303   146  0.88  18.60   1.00     0.97      11120.61|
|  6:  2.7762 -  2.6135  1315   147  0.88  18.37   0.97     0.94       8672.56|
|  7:  2.6135 -  2.4832  1303   145  0.88  18.45   0.99     0.96       7948.90|
|  8:  2.4832 -  2.3755  1302   141  0.88  18.37   1.00     0.97       7174.71|
|  9:  2.3755 -  2.2844  1290   143  0.89  17.97   1.00     0.96       6323.66|
| 10:  2.2844 -  2.2058  1299   144  0.88  18.00   1.01     0.96       5471.99|
| 11:  2.2058 -  2.1371  1273   148  0.88  18.39   1.00     0.96       5270.67|
| 12:  2.1371 -  2.0761  1299   137  0.89  18.00   1.00     0.99       4838.31|
| 13:  2.0761 -  2.0216  1222   135  0.90  16.88   0.99     0.98       3548.96|
| 14:  2.0216 -  1.9724   592    69  0.94  12.24   0.98     0.96       2326.15|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2326.15 max =        13684.62 mean =      8125.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.95 mean =        16.20|
|phase err.(test): min =        0.00 max =           89.45 mean =        15.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.773)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.33    96.05   15.81    None  None   None       |
|    all(noH): 2823   0      1.33    96.05   15.81    None  None   None       |
|    Sol.    : 438    0      4.51    96.05   41.34    None  None   None       |
|    Mac.    : 2385   0      1.33    94.97   11.12    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:     1.331 -  10.803: 1574   |   5:    48.693 -  58.165:   78        |
|      1:    10.803 -  20.276:  687   |   6:    58.165 -  67.637:   59        |
|      2:    20.276 -  29.748:  163   |   7:    67.637 -  77.110:   29        |
|      3:    29.748 -  39.220:  119   |   8:    77.110 -  86.582:    8        |
|      4:    39.220 -  48.693:   98   |   9:    86.582 -  96.054:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.277 - 5.381
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 316 from: 324
   mapped sites are within: 0.713 - 5.381

peak=   10.132 closest distance to " CB  VAL A 230 " =    1.470
peak=    8.749 closest distance to " CB  VAL A 296 " =    1.562
peak=    7.382 closest distance to " O   HOH Z 130 " =    1.533
peak=    6.674 closest distance to " CD2 LEU A   5 " =    1.349
peak=    6.363 closest distance to " O   HOH Z 103 " =    1.178
peak=    5.721 closest distance to " CD1AILE A 234 " =    1.026
peak=    5.640 closest distance to " CG  PRO A  54 " =    1.535
peak=    5.421 closest distance to " O   HOH Z  70 " =    1.026
peak=    5.224 closest distance to " NE2 GLN A  11 " =    1.062
peak=    5.128 closest distance to " O   HOH Z   7 " =    1.509
peak=    5.061 closest distance to " O  BHOH Z  74 " =    1.096
peak=    5.059 closest distance to " O   HOH Z 246 " =    1.187
peak=    5.019 closest distance to " O   HOH Z  65 " =    1.279
peak=    5.019 closest distance to " O   HOH Z 425 " =    1.706
peak=    4.915 closest distance to " O   HOH Z 427 " =    2.461
peak=    4.815 closest distance to " O   HOH Z 222 " =    1.272
peak=    4.800 closest distance to " O   HOH Z 124 " =    1.302
peak=    4.799 closest distance to " CB  ASN A 142 " =    1.017
peak=    4.767 closest distance to " O   HOH Z 127 " =    1.153
peak=    4.748 closest distance to " NH2AARG A 145 " =    1.103
peak=    4.744 closest distance to " O   HOH Z 142 " =    2.004
peak=    4.725 closest distance to " O   HOH Z 255 " =    0.862
peak=    4.698 closest distance to " O   HOH Z  69 " =    1.377
peak=    4.682 closest distance to " CB  ASN A 148 " =    1.410
peak=    4.670 closest distance to " O   HOH Z 258 " =    1.281
peak=    4.661 closest distance to " CG  LEU A 228 " =    1.244
peak=    4.655 closest distance to " O   HOH Z 369 " =    2.170
peak=    4.638 closest distance to " O   HOH Z 232 " =    2.254
peak=    4.610 closest distance to " O   HOH Z  49 " =    1.262
peak=    4.575 closest distance to " CB  VAL A 230 " =    1.270
peak=    4.537 closest distance to " CB  GLN A 223 " =    1.585
peak=    4.511 closest distance to " CB  ARG A 275 " =    0.942
peak=    4.490 closest distance to " O   HOH Z 248 " =    1.195
peak=    4.457 closest distance to " CH2 TRP A 266 " =    1.223
peak=    4.426 closest distance to " NH2 ARG A  56 " =    1.928
peak=    4.423 closest distance to " O   HOH Z 417 " =    1.689
peak=    4.411 closest distance to " O   HOH Z 236 " =    1.581
peak=    4.379 closest distance to " CG  LEU A   5 " =    1.351
peak=    4.375 closest distance to " O   HOH Z 112 " =    1.175
peak=    4.374 closest distance to " CG2 ILE A 234 " =    1.046
peak=    4.371 closest distance to " O   HOH Z 423 " =    1.690
peak=    4.328 closest distance to " CB  PRO A  54 " =    1.059
peak=    4.308 closest distance to " CD  LYS A  76 " =    1.748
peak=    4.288 closest distance to " CB  SER A  63 " =    1.244
peak=    4.274 closest distance to " CG AARG A 275 " =    1.289
peak=    4.259 closest distance to " O   HOH Z 143 " =    1.540
peak=    4.254 closest distance to " O   HOH Z   9 " =    2.526
peak=    4.246 closest distance to " CG  PRO A 243 " =    1.190
peak=    4.243 closest distance to " CB  SER A   3 " =    1.405
peak=    4.238 closest distance to " O   SER A  87 " =    2.408
peak=    4.233 closest distance to " O   HOH Z 331 " =    1.164
peak=    4.202 closest distance to " O   PRO A 198 " =    1.539
peak=    4.199 closest distance to " CG  LEU A 167 " =    1.212
peak=    4.194 closest distance to " CA  PHE A 283 " =    1.165
peak=    4.176 closest distance to " CB AVAL A  41 " =    0.923
peak=    4.136 closest distance to " O   HOH Z 389 " =    1.588
peak=    4.129 closest distance to " O   HOH Z 287 " =    1.952
peak=    4.118 closest distance to " CG2 VAL A 257 " =    0.970
peak=    4.117 closest distance to " O   HOH Z  78 " =    1.706
peak=    4.087 closest distance to " CG  PRO A 198 " =    1.315
peak=    4.062 closest distance to " CG  GLN A  58 " =    1.212
peak=    4.048 closest distance to " O   HOH Z 362 " =    2.335
peak=    4.044 closest distance to " O   HOH Z 365 " =    3.020
peak=    4.043 closest distance to " O   HOH Z 126 " =    1.892
peak=    4.032 closest distance to " CB  SER A 216 " =    1.016
peak=    4.029 closest distance to " O   HOH Z 193 " =    1.574
peak=    4.028 closest distance to " O   HOH Z 211 " =    1.283
peak=    4.000 closest distance to " O   HOH Z 385 " =    1.143
peak=    3.993 closest distance to " O   HOH Z 427 " =    1.299
peak=    3.978 closest distance to " O   HOH Z 123 " =    1.251
peak=    3.964 closest distance to " O   HOH Z 303 " =    2.132
peak=    3.960 closest distance to " C   GLN A  73 " =    1.143
peak=    3.950 closest distance to " O   HOH Z 258 " =    1.825
peak=    3.942 closest distance to " NH2AARG A 190 " =    1.905
peak=    3.933 closest distance to " CB  VAL A 265 " =    1.430
peak=    3.932 closest distance to " O   HOH Z  39 " =    1.272
peak=    3.910 closest distance to " O   HOH Z 380 " =    1.792
peak=    3.903 closest distance to " O   HOH Z 406 " =    1.588
peak=    3.895 closest distance to " O   HOH Z 145 " =    1.621
peak=    3.893 closest distance to " CD2 TRP A 179 " =    1.312
peak=    3.891 closest distance to " O   HOH Z  66 " =    2.350
peak=    3.885 closest distance to " O   HOH Z 248 " =    1.643
peak=    3.867 closest distance to " ND2BASN A 224 " =    0.809
peak=    3.864 closest distance to " O   HOH Z   3 " =    2.302
peak=    3.857 closest distance to " O   HOH Z 403 " =    1.602
peak=    3.857 closest distance to " CB  GLN A 183 " =    1.188
peak=    3.848 closest distance to " ND2 ASN A 187 " =    1.829
peak=    3.847 closest distance to " O   HOH Z 203 " =    1.605
peak=    3.844 closest distance to " CB  ASP A 107 " =    1.102
peak=    3.842 closest distance to " CA  ALA A  51 " =    0.981
peak=    3.841 closest distance to " CB  SER A  62 " =    0.976
peak=    3.835 closest distance to " O   HOH Z 359 " =    1.675
peak=    3.834 closest distance to " N   ASP A 162 " =    1.120
peak=    3.833 closest distance to " CB  ASN A  39 " =    0.961
peak=    3.820 closest distance to " O   HOH Z 251 " =    1.622
peak=    3.812 closest distance to " CD2 LEU A 228 " =    1.253
peak=    3.782 closest distance to " CB  TRP A 179 " =    1.375
peak=    3.773 closest distance to " O   HOH Z 346 " =    1.478
peak=    3.773 closest distance to " O   HOH Z  59 " =    1.720
peak=    3.766 closest distance to " CB  VAL A 202 " =    1.593
peak=    3.766 closest distance to " CG  PRO A 213 " =    1.274
peak=    3.759 closest distance to " O   HOH Z 126 " =    1.567
peak=    3.759 closest distance to " O  BHOH Z 338 " =    2.391
peak=    3.755 closest distance to " O   HOH Z 368 " =    3.120
peak=    3.748 closest distance to " O   HOH Z 411 " =    3.391
peak=    3.744 closest distance to " CB  PRO A  90 " =    1.114
peak=    3.741 closest distance to " O   HOH Z 153 " =    3.742
peak=    3.739 closest distance to " CB  ASP A 124 " =    0.816
peak=    3.733 closest distance to " CB  ASN A 215 " =    1.187
peak=    3.721 closest distance to " ND2 ASN A 249 " =    0.945
peak=    3.717 closest distance to " NE AARG A 145 " =    0.813
peak=    3.712 closest distance to " O   HOH Z 158 " =    2.718
peak=    3.706 closest distance to " O   HOH Z 423 " =    1.567
peak=    3.701 closest distance to " O   HOH Z 263 " =    1.425
peak=    3.686 closest distance to " O   HOH Z 272 " =    1.834
peak=    3.676 closest distance to " NH1AARG A 145 " =    1.129
peak=    3.675 closest distance to " CE  LYS A  76 " =    0.928
peak=    3.672 closest distance to " O   HOH Z 116 " =    1.094
peak=    3.668 closest distance to " OG ASER A 258 " =    3.012
peak=    3.643 closest distance to " CB  ALA A 114 " =    0.977
peak=    3.642 closest distance to " O   HOH Z  61 " =    1.652
peak=    3.641 closest distance to " CB  SER A 276 " =    1.165
peak=    3.638 closest distance to " CB  SER A 212 " =    1.505
peak=    3.631 closest distance to " O   HOH Z 298 " =    1.628
peak=    3.628 closest distance to " CD  ARG A  66 " =    2.696
peak=    3.626 closest distance to " O   HOH Z  26 " =    1.292
peak=    3.622 closest distance to " CA  ARG A 195 " =    1.221
peak=    3.617 closest distance to " CA  ASP A 162 " =    0.742
peak=    3.615 closest distance to " N   PHE A 130 " =    1.359
peak=    3.615 closest distance to " O   TYR A 116 " =    1.179
peak=    3.613 closest distance to " CG  ARG A 138 " =    1.268
peak=    3.612 closest distance to " CB  GLN A  89 " =    1.105
peak=    3.608 closest distance to " CB  SER A  26 " =    1.650
peak=    3.600 closest distance to " CB  GLU A 277 " =    3.505
peak=    3.599 closest distance to " O   HOH Z 402 " =    1.417
peak=    3.593 closest distance to " O   HOH Z  80 " =    1.630
peak=    3.591 closest distance to " CB  TYR A 169 " =    0.824
peak=    3.590 closest distance to " O   HOH Z 419 " =    1.849
peak=    3.589 closest distance to " CG2 ILE A  20 " =    1.617
peak=    3.588 closest distance to " CD1 ILE A 199 " =    1.242
peak=    3.585 closest distance to " CB  ALA A 160 " =    1.504
peak=    3.578 closest distance to " O   PHE A 192 " =    1.345
peak=    3.575 closest distance to " CB  ALA A  43 " =    0.888
peak=    3.570 closest distance to " CA  TYR A  30 " =    1.033
peak=    3.569 closest distance to " CA  TRP A 150 " =    0.736
peak=    3.567 closest distance to " O   HOH Z 207 " =    1.214
peak=    3.566 closest distance to " CA  ALA A 100 " =    0.852
peak=    3.565 closest distance to " CB  GLU A 152 " =    1.216
peak=    3.562 closest distance to " CB  ARG A  79 " =    0.801
peak=    3.536 closest distance to " CG  LYS A 119 " =    0.964
peak=    3.534 closest distance to " O   HOH Z 422 " =    2.482
peak=    3.531 closest distance to " O   HOH Z  40 " =    1.881
peak=    3.518 closest distance to " CA  SER A  87 " =    0.956
peak=    3.511 closest distance to " O   HOH Z   1 " =    1.933
peak=    3.506 closest distance to " O   HOH Z 214 " =    2.560
peak=    3.497 closest distance to " CE3 TRP A 150 " =    1.114
peak=    3.496 closest distance to " CA  ARG A 159 " =    1.179
peak=    3.496 closest distance to " OG BSER A 212 " =    2.689
peak=    3.493 closest distance to " O   HOH Z 403 " =    1.451
peak=    3.489 closest distance to " O   HOH Z 281 " =    2.207
peak=    3.483 closest distance to " CZ  PHE A 218 " =    1.148
peak=    3.482 closest distance to " CG2 ILE A 120 " =    1.205
peak=    3.476 closest distance to " O   HOH Z 193 " =    1.597
peak=    3.475 closest distance to " O   HOH Z 437 " =    1.768
peak=    3.467 closest distance to " CD1 LEU A  96 " =    0.926
peak=    3.460 closest distance to " CA  ALA A 129 " =    1.159
peak=    3.457 closest distance to " CD  ARG A 269 " =    1.030
peak=    3.454 closest distance to " CB  LEU A 300 " =    1.044
peak=    3.448 closest distance to " CB  ARG A 138 " =    0.887
peak=    3.439 closest distance to " CB  ARG A 156 " =    1.114
peak=    3.430 closest distance to " O   HOH Z 329 " =    4.236
peak=    3.425 closest distance to " O   HOH Z 132 " =    2.307
peak=    3.421 closest distance to " O   HOH Z  10 " =    1.616
peak=    3.419 closest distance to " CD1 ILE A  33 " =    1.828
peak=    3.417 closest distance to " O   HOH Z 222 " =    2.199
peak=    3.413 closest distance to " N   ARG A 156 " =    1.362
peak=    3.413 closest distance to " CA  ILE A 234 " =    1.079
peak=    3.410 closest distance to " N   ASN A  39 " =    1.140
peak=    3.405 closest distance to " O   HOH Z  85 " =    1.218
peak=    3.405 closest distance to " O   HOH Z 234 " =    3.603
peak=    3.402 closest distance to " CD1 LEU A   5 " =    1.562
peak=    3.396 closest distance to " O   HOH Z 357 " =    2.046
peak=    3.396 closest distance to " CB  PHE A 204 " =    0.828
peak=    3.394 closest distance to " N   ALA A 256 " =    1.130
peak=    3.384 closest distance to " O   HOH Z 180 " =    2.201
peak=    3.380 closest distance to " CB  ASN A 148 " =    2.005
peak=    3.379 closest distance to " NZ  LYS A 117 " =    1.217
peak=    3.379 closest distance to " CB  LYS A 117 " =    1.247
peak=    3.365 closest distance to " CB  ASN A 110 " =    1.093
peak=    3.364 closest distance to " CD2 TYR A 186 " =    1.054
peak=    3.362 closest distance to " O   HOH Z 414 " =    1.292
peak=    3.360 closest distance to " CA  GLN A  58 " =    0.922
peak=    3.357 closest distance to " O   HOH Z 368 " =    2.247
peak=    3.349 closest distance to " CD1 LEU A 281 " =    1.044
peak=    3.347 closest distance to " O   HOH Z 265 " =    1.855
peak=    3.347 closest distance to " O   HOH Z 148 " =    1.482
peak=    3.344 closest distance to " O   HOH Z 423 " =    2.037
peak=    3.341 closest distance to " ND2 ASN A 176 " =    0.844
peak=    3.340 closest distance to " O   HOH Z  54 " =    1.562
peak=    3.335 closest distance to " O   HOH Z 270 " =    1.457
peak=    3.325 closest distance to " N   ASN A 127 " =    1.323
peak=    3.322 closest distance to " O   HOH Z  61 " =    1.822
peak=    3.320 closest distance to " O   HOH Z  43 " =    1.952
peak=    3.320 closest distance to " O   PRO A 198 " =    1.546
peak=    3.315 closest distance to " O   HOH Z 415 " =    3.523
peak=    3.314 closest distance to " O   HOH Z 325 " =    2.178
peak=    3.310 closest distance to " OG  SER A  62 " =    2.380
peak=    3.310 closest distance to " O   HOH Z 184 " =    1.465
peak=    3.309 closest distance to " CG1BVAL A  72 " =    1.441
peak=    3.305 closest distance to " OG  SER A 276 " =    1.007
peak=    3.301 closest distance to " CA  ASN A 215 " =    1.073
peak=    3.299 closest distance to " O   HOH Z 218 " =    1.605
peak=    3.297 closest distance to " O   HOH Z  24 " =    1.858
peak=    3.296 closest distance to " CG1BVAL A  72 " =    0.820
peak=    3.292 closest distance to " OG  SER A  62 " =    3.025
peak=    3.290 closest distance to " CG2 ILE A 239 " =    0.713
peak=    3.290 closest distance to " O   HOH Z 280 " =    2.949
peak=    3.288 closest distance to " O   THR A 182 " =    1.433
peak=    3.287 closest distance to " O   HOH Z 216 " =    3.542
peak=    3.286 closest distance to " CB  ARG A 145 " =    0.913
peak=    3.279 closest distance to " CG1 VAL A 257 " =    1.408
peak=    3.274 closest distance to " CA  LEU A 282 " =    1.255
peak=    3.273 closest distance to " O   HOH Z 379 " =    1.509
peak=    3.272 closest distance to " OE2 GLU A   2 " =    2.026
peak=    3.269 closest distance to " CB  GLN A 278 " =    1.000
peak=    3.264 closest distance to " O   HOH Z 323 " =    1.590
peak=    3.258 closest distance to " NE1 TRP A  92 " =    1.745
peak=    3.256 closest distance to " OE2 GLU A  53 " =    1.938
peak=    3.255 closest distance to " O   ASN A 209 " =    1.366
peak=    3.252 closest distance to " OG1 THR A 221 " =    1.123
peak=    3.252 closest distance to " O   HOH Z  51 " =    1.597
peak=    3.251 closest distance to " CB  SER A 210 " =    0.800
peak=    3.250 closest distance to " CB  GLN A  88 " =    1.253
peak=    3.244 closest distance to " O   HOH Z 220 " =    1.663
peak=    3.241 closest distance to " CB  ALA A  10 " =    0.733
peak=    3.235 closest distance to " N   TRP A  70 " =    0.794
peak=    3.234 closest distance to " CB  TYR A 116 " =    0.913
peak=    3.233 closest distance to " CB  ASN A 187 " =    1.138
peak=    3.229 closest distance to " CA  MET A 105 " =    0.914
peak=    3.229 closest distance to " O   HOH Z 272 " =    2.378
peak=    3.228 closest distance to " OG BSER A 164 " =    2.274
peak=    3.223 closest distance to " O   HOH Z  71 " =    1.423
peak=    3.219 closest distance to " NZ  LYS A  48 " =    1.297
peak=    3.218 closest distance to " CA  ALA A 291 " =    0.835
peak=    3.215 closest distance to " CG1 VAL A 153 " =    0.820
peak=    3.215 closest distance to " O   HOH Z 438 " =    2.436
peak=    3.213 closest distance to " O   HOH Z 188 " =    2.758
peak=    3.213 closest distance to " O   HOH Z 158 " =    0.984
peak=    3.213 closest distance to " NH1 ARG A  14 " =    1.091
peak=    3.213 closest distance to " O   HOH Z 117 " =    1.993
peak=    3.207 closest distance to " O   HOH Z 146 " =    1.380
peak=    3.206 closest distance to " O   HOH Z 324 " =    1.442
peak=    3.205 closest distance to " O   HOH Z 144 " =    1.658
peak=    3.205 closest distance to " O   HOH Z  21 " =    1.632
peak=    3.201 closest distance to " CA  ALA A 154 " =    1.090
peak=    3.201 closest distance to " O   HOH Z 405 " =    1.641
peak=    3.200 closest distance to " CB  TRP A 266 " =    1.074
peak=    3.199 closest distance to " O   HOH Z  40 " =    1.866
peak=    3.199 closest distance to " O   HOH Z  78 " =    1.978
peak=    3.197 closest distance to " O   HOH Z 293 " =    1.488
peak=    3.194 closest distance to " CB  THR A  31 " =    1.441
peak=    3.191 closest distance to " CA  ASN A 127 " =    1.075
peak=    3.190 closest distance to " N   CYS A 260 " =    0.837
peak=    3.188 closest distance to " O   HOH Z 424 " =    2.622
peak=    3.185 closest distance to " N   SER A 135 " =    1.367
peak=    3.179 closest distance to " O   HOH Z  76 " =    1.337
peak=    3.177 closest distance to " CA  GLY A 136 " =    0.920
peak=    3.176 closest distance to " O   HOH Z 218 " =    1.803
peak=    3.175 closest distance to " O   HOH Z  22 " =    1.925
peak=    3.172 closest distance to " N   GLN A 278 " =    1.198
peak=    3.171 closest distance to " O   HOH Z 172 " =    5.381
peak=    3.167 closest distance to " CZ3 TRP A 177 " =    1.148
peak=    3.166 closest distance to " NE2 HIS A 207 " =    1.046
peak=    3.165 closest distance to " O   HOH Z 213 " =    1.852
peak=    3.160 closest distance to " CA  ASN A 217 " =    1.182
peak=    3.158 closest distance to " N   GLN A 122 " =    0.820
peak=    3.156 closest distance to " O   HOH Z 189 " =    3.220
peak=    3.155 closest distance to " NZ  LYS A 117 " =    2.887
peak=    3.155 closest distance to " CB  ARG A  79 " =    1.276
peak=    3.154 closest distance to " CZ  PHE A  38 " =    1.085
peak=    3.154 closest distance to " NE1 TRP A  85 " =    1.198
peak=    3.149 closest distance to " ND1 HIS A  86 " =    1.716
peak=    3.149 closest distance to " CA  ALA A 184 " =    1.088
peak=    3.143 closest distance to " CB  ALA A 291 " =    0.753
peak=    3.140 closest distance to " O   HOH Z 343 " =    3.119
peak=    3.138 closest distance to " O   HOH Z  27 " =    1.089
peak=    3.138 closest distance to " O   HOH Z 132 " =    2.840
peak=    3.137 closest distance to " O   HOH Z 425 " =    2.030
peak=    3.137 closest distance to " CB  TYR A  30 " =    1.461
peak=    3.137 closest distance to " CB  MET A  40 " =    0.846
peak=    3.137 closest distance to " CG BARG A 102 " =    1.962
peak=    3.137 closest distance to " O   HOH Z 261 " =    1.999
peak=    3.134 closest distance to " CB  HIS A 108 " =    0.827
peak=    3.134 closest distance to " O   HOH Z 238 " =    1.320
peak=    3.132 closest distance to " O   HOH Z   1 " =    1.704
peak=    3.130 closest distance to " O   HOH Z 343 " =    2.624
peak=    3.130 closest distance to " OG  SER A 135 " =    1.305
peak=    3.128 closest distance to " CG  GLN A  77 " =    0.974
peak=    3.126 closest distance to " CA  SER A 210 " =    1.423
peak=    3.124 closest distance to " CD  GLN A  77 " =    1.292
peak=    3.122 closest distance to " O   HOH Z  83 " =    1.320
peak=    3.120 closest distance to " CE3 TRP A 274 " =    1.303
peak=    3.090 closest distance to " O   HOH Z 225 " =    1.821
peak=    3.087 closest distance to " NE2 GLN A  58 " =    4.663
peak=    3.084 closest distance to " CG2BVAL A 121 " =    0.731
peak=    3.079 closest distance to " OD1 ASN A 301 " =    1.485
peak=    3.078 closest distance to " OH  TYR A 214 " =    1.759
peak=    3.077 closest distance to " CG  GLU A  37 " =    0.982
peak=    3.065 closest distance to " O   LYS A  48 " =    1.229
peak=    3.062 closest distance to " O   HOH Z 162 " =    1.349
peak=    3.059 closest distance to " CZ3 TRP A  92 " =    1.236
peak=    3.059 closest distance to " O   HOH Z 383 " =    1.854
peak=    3.051 closest distance to " O   HOH Z 222 " =    2.007
peak=    3.049 closest distance to " O   HOH Z 371 " =    2.734
peak=    3.040 closest distance to " O   HOH Z  99 " =    1.867
peak=    3.022 closest distance to " CB  ASN A 173 " =    0.904

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.583 - 5.629
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 198
   mapped sites are within: 0.719 - 5.629

peak=   -5.091 closest distance to " O   PRO A 198 " =    1.172
peak=   -4.653 closest distance to " O   HOH Z  69 " =    1.454
peak=   -4.398 closest distance to " O   HOH Z 231 " =    0.809
peak=   -4.292 closest distance to " O   HOH Z 100 " =    0.802
peak=   -4.204 closest distance to " CB  GLN A  55 " =    1.226
peak=   -4.158 closest distance to " O   HOH Z 387 " =    2.564
peak=   -4.108 closest distance to " O   HOH Z 131 " =    4.131
peak=   -4.106 closest distance to " CD  ARG A  14 " =    3.005
peak=   -4.074 closest distance to " O   VAL A  67 " =    2.422
peak=   -4.047 closest distance to " O   HOH Z 147 " =    1.929
peak=   -3.992 closest distance to " CZ2 TRP A  92 " =    2.795
peak=   -3.991 closest distance to " O   HOH Z 276 " =    1.103
peak=   -3.945 closest distance to " O   HOH Z  60 " =    1.699
peak=   -3.942 closest distance to " CD  ARG A 156 " =    1.918
peak=   -3.905 closest distance to " O   HOH Z 359 " =    3.135
peak=   -3.905 closest distance to " CD1 LEU A 101 " =    2.321
peak=   -3.855 closest distance to " O   HOH Z 134 " =    4.392
peak=   -3.838 closest distance to " CB  VAL A 230 " =    1.032
peak=   -3.817 closest distance to " C   HIS A 108 " =    1.200
peak=   -3.799 closest distance to " CD  PRO A 213 " =    2.052
peak=   -3.799 closest distance to " O   HOH Z 411 " =    5.361
peak=   -3.765 closest distance to " O   HOH Z 203 " =    1.258
peak=   -3.763 closest distance to " NE2 GLN A  55 " =    1.095
peak=   -3.749 closest distance to " CD1 LEU A 255 " =    2.886
peak=   -3.726 closest distance to " CB  ALA A  43 " =    2.494
peak=   -3.712 closest distance to " O   HOH Z 144 " =    1.054
peak=   -3.709 closest distance to " CG  GLN A  58 " =    1.106
peak=   -3.697 closest distance to " CG2 ILE A  20 " =    2.785
peak=   -3.696 closest distance to " O   HOH Z 255 " =    2.519
peak=   -3.693 closest distance to " O   SER A 135 " =    1.583
peak=   -3.680 closest distance to " O   HOH Z 368 " =    1.222
peak=   -3.671 closest distance to " O   HOH Z  66 " =    0.891
peak=   -3.669 closest distance to " OG BSER A 134 " =    1.464
peak=   -3.668 closest distance to " O   HOH Z 389 " =    1.403
peak=   -3.660 closest distance to " CE2 TYR A  30 " =    2.638
peak=   -3.658 closest distance to " CB  ASP A 132 " =    2.431
peak=   -3.653 closest distance to " O   HOH Z 398 " =    0.896
peak=   -3.653 closest distance to " O   SER A 276 " =    1.603
peak=   -3.645 closest distance to " O   HOH Z  39 " =    1.045
peak=   -3.638 closest distance to " O   ILE A  49 " =    1.687
peak=   -3.624 closest distance to " SG BCYS A 201 " =    2.236
peak=   -3.622 closest distance to " CG2 VAL A 202 " =    2.753
peak=   -3.612 closest distance to " CG2 VAL A 189 " =    1.956
peak=   -3.611 closest distance to " C   ARG A 269 " =    1.392
peak=   -3.609 closest distance to " O   HOH Z  70 " =    0.942
peak=   -3.601 closest distance to " CG1 VAL A 250 " =    2.778
peak=   -3.590 closest distance to " CG  ARG A 219 " =    2.435
peak=   -3.585 closest distance to " CG  TRP A 266 " =    1.719
peak=   -3.582 closest distance to " CD1 ILE A 151 " =    2.539
peak=   -3.568 closest distance to " OG  SER A  97 " =    2.319
peak=   -3.566 closest distance to " O   ALA A  51 " =    1.243
peak=   -3.561 closest distance to " CA  GLY A 241 " =    2.410
peak=   -3.560 closest distance to " CB  ALA A   7 " =    2.091
peak=   -3.547 closest distance to " O   GLN A 144 " =    1.328
peak=   -3.536 closest distance to " CD2 TYR A 293 " =    2.002
peak=   -3.523 closest distance to " CB  ALA A 248 " =    2.148
peak=   -3.522 closest distance to " CD  LYS A 289 " =    2.315
peak=   -3.516 closest distance to " O  BHOH Z  74 " =    0.879
peak=   -3.506 closest distance to " O   HOH Z 275 " =    1.718
peak=   -3.500 closest distance to " CZ  TYR A 169 " =    1.846
peak=   -3.499 closest distance to " OE1 GLN A  88 " =    1.030
peak=   -3.496 closest distance to " CA  GLN A  58 " =    1.128
peak=   -3.492 closest distance to " O   GLU A 152 " =    1.517
peak=   -3.488 closest distance to " O   HOH Z  71 " =    1.188
peak=   -3.485 closest distance to " CD2 LEU A   5 " =    0.961
peak=   -3.485 closest distance to " O   HOH Z 286 " =    1.490
peak=   -3.478 closest distance to " O   HOH Z 111 " =    1.875
peak=   -3.468 closest distance to " O   PRO A 163 " =    1.955
peak=   -3.456 closest distance to " CD2 LEU A 237 " =    2.754
peak=   -3.455 closest distance to " NZ  LYS A 166 " =    1.260
peak=   -3.454 closest distance to " O   HOH Z 255 " =    0.939
peak=   -3.454 closest distance to " CD2 HIS A 207 " =    2.230
peak=   -3.442 closest distance to " O   HOH Z  44 " =    1.074
peak=   -3.435 closest distance to " NH2 ARG A  79 " =    2.096
peak=   -3.434 closest distance to " O   HOH Z  53 " =    1.451
peak=   -3.432 closest distance to " O   HOH Z 427 " =    1.905
peak=   -3.431 closest distance to " ND2 ASN A 285 " =    2.107
peak=   -3.422 closest distance to " O   HOH Z  64 " =    1.195
peak=   -3.420 closest distance to " O   HOH Z 231 " =    2.018
peak=   -3.419 closest distance to " O   HOH Z 238 " =    0.897
peak=   -3.415 closest distance to " CA  ASP A  27 " =    2.422
peak=   -3.410 closest distance to " O   HOH Z 295 " =    1.649
peak=   -3.409 closest distance to " OE1 GLU A 277 " =    2.243
peak=   -3.400 closest distance to " O   HOH Z 278 " =    1.047
peak=   -3.398 closest distance to " O   SER A  22 " =    2.485
peak=   -3.396 closest distance to " O   HOH Z  26 " =    0.797
peak=   -3.395 closest distance to " CA  HIS A 207 " =    1.165
peak=   -3.388 closest distance to " CD  GLN A  88 " =    1.249
peak=   -3.387 closest distance to " CE  MET A 188 " =    2.160
peak=   -3.385 closest distance to " CZ  PHE A  38 " =    2.409
peak=   -3.377 closest distance to " NE2 GLN A 223 " =    1.812
peak=   -3.375 closest distance to " C   ASN A 285 " =    2.101
peak=   -3.375 closest distance to " OE1 GLU A  44 " =    0.995
peak=   -3.374 closest distance to " C   MET A 188 " =    1.506
peak=   -3.374 closest distance to " O   HOH Z 116 " =    1.513
peak=   -3.368 closest distance to " NE2 GLN A  11 " =    1.702
peak=   -3.363 closest distance to " O   HOH Z 235 " =    1.227
peak=   -3.361 closest distance to " ND2 ASN A  45 " =    2.287
peak=   -3.360 closest distance to " C   GLN A 205 " =    1.949
peak=   -3.353 closest distance to " O   HOH Z 394 " =    1.560
peak=   -3.350 closest distance to " O   HOH Z 147 " =    1.127
peak=   -3.347 closest distance to " O   HOH Z 109 " =    0.906
peak=   -3.347 closest distance to " O   HOH Z 371 " =    1.323
peak=   -3.343 closest distance to " C   GLU A   2 " =    1.843
peak=   -3.340 closest distance to " CG1BVAL A  72 " =    5.236
peak=   -3.336 closest distance to " CE1 TYR A 186 " =    2.352
peak=   -3.335 closest distance to " CB  ALA A 114 " =    2.579
peak=   -3.333 closest distance to " O   HOH Z 351 " =    1.654
peak=   -3.323 closest distance to " O   HOH Z 377 " =    0.719
peak=   -3.320 closest distance to " O   HOH Z 290 " =    1.114
peak=   -3.320 closest distance to " N   PHE A  59 " =    1.974
peak=   -3.319 closest distance to " CG1 VAL A 125 " =    2.340
peak=   -3.319 closest distance to " CZ  ARG A 259 " =    0.828
peak=   -3.318 closest distance to " CG1 VAL A 112 " =    2.641
peak=   -3.318 closest distance to " ND2 ASN A 187 " =    1.253
peak=   -3.318 closest distance to " OG  SER A  62 " =    4.073
peak=   -3.317 closest distance to " NE2 GLN A 278 " =    1.857
peak=   -3.310 closest distance to " CG2BVAL A  72 " =    1.880
peak=   -3.309 closest distance to " CB  ALA A 161 " =    1.586
peak=   -3.307 closest distance to " CB  TRP A  85 " =    2.529
peak=   -3.300 closest distance to " O   HOH Z 105 " =    1.119
peak=   -3.293 closest distance to " O   HOH Z 191 " =    5.629
peak=   -3.292 closest distance to " CG2 ILE A 151 " =    2.462
peak=   -3.289 closest distance to " O   HOH Z 149 " =    2.064
peak=   -3.285 closest distance to " CG2 VAL A 296 " =    2.188
peak=   -3.282 closest distance to " CD  PRO A 243 " =    1.857
peak=   -3.281 closest distance to " O   HOH Z 331 " =    0.887
peak=   -3.278 closest distance to " ND2 ASN A 173 " =    1.578
peak=   -3.277 closest distance to " C   VAL A  72 " =    0.859
peak=   -3.273 closest distance to " CB  PRO A 163 " =    2.327
peak=   -3.268 closest distance to " CZ2 TRP A 274 " =    1.001
peak=   -3.265 closest distance to " CD2 TYR A 247 " =    2.527
peak=   -3.263 closest distance to " O   SER A 271 " =    2.091
peak=   -3.255 closest distance to " CE1 TYR A 247 " =    2.527
peak=   -3.255 closest distance to " O   HOH Z 257 " =    0.903
peak=   -3.245 closest distance to " CB  ALA A  10 " =    2.296
peak=   -3.243 closest distance to " O   HOH Z 312 " =    1.526
peak=   -3.240 closest distance to " CG  MET A 105 " =    0.968
peak=   -3.238 closest distance to " CA  GLY A  98 " =    1.934
peak=   -3.231 closest distance to " CD1 LEU A 228 " =    2.150
peak=   -3.228 closest distance to " CB  ALA A 161 " =    2.396
peak=   -3.226 closest distance to " CG2 THR A 178 " =    2.320
peak=   -3.221 closest distance to " O   HOH Z 414 " =    1.110
peak=   -3.221 closest distance to " O   HOH Z 281 " =    2.749
peak=   -3.220 closest distance to " O   LEU A  83 " =    2.751
peak=   -3.220 closest distance to " O   ASP A 298 " =    1.970
peak=   -3.219 closest distance to " O   HOH Z 105 " =    2.849
peak=   -3.216 closest distance to " O   HOH Z 285 " =    2.025
peak=   -3.205 closest distance to " CD1 ILE A 151 " =    2.087
peak=   -3.204 closest distance to " O   HOH Z 374 " =    1.965
peak=   -3.199 closest distance to " O   HOH Z 198 " =    1.324
peak=   -3.196 closest distance to " CE2 TRP A  70 " =    2.445
peak=   -3.194 closest distance to " CB  SER A 210 " =    1.075
peak=   -3.194 closest distance to " O   HOH Z 368 " =    2.484
peak=   -3.193 closest distance to " CA  GLY A 133 " =    1.893
peak=   -3.192 closest distance to " CG2 THR A 221 " =    2.146
peak=   -3.192 closest distance to " N   ALA A 244 " =    1.305
peak=   -3.190 closest distance to " OE1 GLN A 223 " =    1.969
peak=   -3.190 closest distance to " CB  TYR A  68 " =    1.586
peak=   -3.190 closest distance to " O   HOH Z 107 " =    0.885
peak=   -3.189 closest distance to " O   HOH Z 216 " =    1.574
peak=   -3.185 closest distance to " CA  LEU A   5 " =    2.693
peak=   -3.181 closest distance to " O   HOH Z 389 " =    2.406
peak=   -3.180 closest distance to " CD  GLN A 223 " =    1.210
peak=   -3.177 closest distance to " O   ALA A  10 " =    1.616
peak=   -3.174 closest distance to " O   HOH Z 298 " =    3.215
peak=   -3.165 closest distance to " O   HOH Z 384 " =    1.711
peak=   -3.164 closest distance to " O   HOH Z  83 " =    1.273
peak=   -3.161 closest distance to " CD  GLN A  77 " =    1.069
peak=   -3.161 closest distance to " O   HOH Z 162 " =    2.744
peak=   -3.157 closest distance to " OD2 ASP A 171 " =    2.289
peak=   -3.154 closest distance to " O   HOH Z 126 " =    1.764
peak=   -3.154 closest distance to " O   HOH Z 165 " =    2.168
peak=   -3.151 closest distance to " O   HOH Z  32 " =    2.006
peak=   -3.144 closest distance to " O   HOH Z 236 " =    1.293
peak=   -3.141 closest distance to " O   HOH Z 105 " =    1.825
peak=   -3.139 closest distance to " O   SER A 210 " =    1.900
peak=   -3.134 closest distance to " O   HOH Z 201 " =    2.149
peak=   -3.133 closest distance to " CG1 VAL A 197 " =    2.322
peak=   -3.133 closest distance to " CG2 ILE A 263 " =    2.330
peak=   -3.132 closest distance to " N   ALA A  43 " =    2.548
peak=   -3.126 closest distance to " O   HOH Z  11 " =    1.556
peak=   -3.125 closest distance to " CG1 VAL A 265 " =    2.509
peak=   -3.105 closest distance to " O   HOH Z 158 " =    1.810
peak=   -3.101 closest distance to " OE2 GLU A 152 " =    1.273
peak=   -3.094 closest distance to " CE2 PHE A 218 " =    2.526
peak=   -3.084 closest distance to " CG  ASP A 231 " =    0.804
peak=   -3.065 closest distance to " CG  GLN A 103 " =    2.302
peak=   -3.046 closest distance to " NH2 ARG A 219 " =    1.738
peak=   -3.040 closest distance to " OG1 THR A  82 " =    1.084
peak=   -3.011 closest distance to " CG  ARG A 219 " =    2.158

================= 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    :  0.5029 0.4903   6.300084e+00   6.287211e+00
   1_bss:  0.4941 0.4786   6.293841e+00   6.277981e+00
   1_xyz:  0.4279 0.4492   6.220880e+00   6.239233e+00
   1_adp:  0.3874 0.4479   6.167588e+00   6.233453e+00
   1_occ:  0.3870 0.4479   6.166954e+00   6.234167e+00
   2_bss:  0.3857 0.4455   6.169127e+00   6.235408e+00
   2_xyz:  0.3201 0.3890   6.027283e+00   6.151472e+00
   2_adp:  0.3001 0.3717   5.988180e+00   6.118564e+00
   2_occ:  0.2999 0.3723   5.988468e+00   6.118780e+00
   3_bss:  0.2994 0.3720   5.988959e+00   6.119276e+00
   3_xyz:  0.2204 0.2849   5.729778e+00   5.924520e+00
   3_adp:  0.1953 0.2584   5.627244e+00   5.836167e+00
   3_occ:  0.1950 0.2578   5.625566e+00   5.834052e+00
   4_bss:  0.1941 0.2574   5.627089e+00   5.835407e+00
   4_xyz:  0.1534 0.2107   5.422385e+00   5.653385e+00
   4_adp:  0.1416 0.2001   5.356522e+00   5.596471e+00
   4_occ:  0.1415 0.1999   5.355628e+00   5.595404e+00
   5_bss:  0.1417 0.2001   5.354824e+00   5.594964e+00
   5_xyz:  0.1295 0.1829   5.281150e+00   5.524258e+00
   5_adp:  0.1283 0.1763   5.261632e+00   5.489096e+00
   5_occ:  0.1281 0.1761   5.260434e+00   5.487794e+00
   5_bss:  0.1281 0.1761   5.260332e+00   5.487701e+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:  0.366  20.000   5.642   7.854  10.726   0.000   0.000   0.000
   1_xyz:  0.366  20.000   5.642   7.854  10.726   0.000   0.000   0.000
   1_adp:  0.366  20.000   5.642   7.854  10.726   0.000   0.000   0.000
   1_occ:  0.366  20.000   5.642   7.854  10.726   0.000   0.000   0.000
   2_bss:  0.346  39.130   3.060   4.390   7.436   0.000   0.000   0.000
   2_xyz:  0.346  39.130   3.060   4.390   7.436   0.000   0.000   0.000
   2_adp:  0.346  39.130   3.060   4.390   7.436   0.000   0.000   0.000
   2_occ:  0.346  39.130   3.060   4.390   7.436   0.000   0.000   0.000
   3_bss:  0.343  57.246   1.619   2.531   5.195   0.000   0.000   0.000
   3_xyz:  0.343  57.246   1.619   2.531   5.195   0.000   0.000   0.000
   3_adp:  0.343  57.246   1.619   2.531   5.195   0.000   0.000   0.000
   3_occ:  0.343  57.246   1.619   2.531   5.195   0.000   0.000   0.000
   4_bss:  0.324  57.246   0.556   1.221   3.526   0.000   0.000   0.000
   4_xyz:  0.324  57.246   0.556   1.221   3.526   0.000   0.000   0.000
   4_adp:  0.324  57.246   0.556   1.221   3.526   0.000   0.000   0.000
   4_occ:  0.324  57.246   0.556   1.221   3.526   0.000   0.000   0.000
   5_bss:  0.327  62.675   0.397   0.817   3.098   0.000   0.000   0.000
   5_xyz:  0.327  62.675   0.397   0.817   3.098   0.000   0.000   0.000
   5_adp:  0.327  62.675   0.397   0.817   3.098   0.000   0.000   0.000
   5_occ:  0.327  62.675   0.397   0.817   3.098   0.000   0.000   0.000
   5_bss:  0.332  64.006  -0.971  -0.629   1.601  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.745 0.3445  0.4099    79157.682
   1_bss:  62.689 0.3576  0.5356    76683.013
   1_xyz:  53.731 0.4724  0.6933    61424.677
   1_adp:  52.011 0.4942  0.7994    59607.031
   1_occ:  52.123 0.4927  0.7955    59754.548
   2_bss:  51.935 0.4951  0.7199    59606.981
   2_xyz:  42.931 0.6060  0.8672    42373.896
   2_adp:  40.242 0.6389  0.9016    38319.414
   2_occ:  40.310 0.6381  0.9002    38395.374
   3_bss:  40.209 0.6392  0.8447    38246.704
   3_xyz:  29.258 0.7648  0.9774    21356.655
   3_adp:  25.471 0.8065  0.9991    17282.180
   3_occ:  25.427 0.8069  0.9989    17180.777
   4_bss:  25.435 0.8069  0.9514    17269.929
   4_xyz:  20.231 0.8592  0.9826    11449.920
   4_adp:  18.792 0.8731  0.9800    10217.560
   4_occ:  18.762 0.8734  0.9802    10191.080
   5_bss:  18.725 0.8737  0.9688    10160.829
   5_xyz:  17.021 0.8893  0.9771     8674.631
   5_adp:  16.163 0.8972  0.9764     8161.182
   5_occ:  16.140 0.8974  0.9765     8129.568
   5_bss:  16.135 0.8974  0.9730     8126.350
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3672e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3672e+01
   1_xyz:   1.741  0.013  0.106 18.363  0.006  4.106   1.4738e-01
   1_adp:   1.741  0.013  0.106 18.363  0.006  4.106   1.4738e-01
   1_occ:   1.741  0.013  0.106 18.363  0.006  4.106   1.4738e-01
   2_bss:   1.741  0.013  0.106 18.363  0.006  4.106   1.4738e-01
   2_xyz:   1.209  0.009  0.080 16.248  0.005  4.107   8.9403e-02
   2_adp:   1.209  0.009  0.080 16.248  0.005  4.107   8.9403e-02
   2_occ:   1.209  0.009  0.080 16.248  0.005  4.107   8.9403e-02
   3_bss:   1.209  0.009  0.080 16.248  0.005  4.107   8.9403e-02
   3_xyz:   1.254  0.010  0.091 16.364  0.005  4.127   9.2305e-02
   3_adp:   1.254  0.010  0.091 16.364  0.005  4.127   9.2305e-02
   3_occ:   1.254  0.010  0.091 16.364  0.005  4.127   9.2305e-02
   4_bss:   1.254  0.010  0.091 16.364  0.005  4.127   9.2305e-02
   4_xyz:   1.098  0.009  0.079 15.876  0.004  4.123   7.3963e-02
   4_adp:   1.098  0.009  0.079 15.876  0.004  4.123   7.3963e-02
   4_occ:   1.098  0.009  0.079 15.876  0.004  4.123   7.3963e-02
   5_bss:   1.098  0.009  0.079 15.876  0.004  4.123   7.3963e-02
   5_xyz:   0.976  0.007  0.073 15.603  0.004  4.117   6.0670e-02
   5_adp:   0.976  0.007  0.073 15.603  0.004  4.117   6.0670e-02
   5_occ:   0.976  0.007  0.073 15.603  0.004  4.117   6.0670e-02
   5_bss:   0.976  0.007  0.073 15.603  0.004  4.117   6.0670e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.138   6.9550e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.138   6.9550e+00
   1_xyz:  14.013  0.176  0.424 85.019  0.036  2.093   1.0151e-01
   1_adp:  14.013  0.176  0.424 85.019  0.036  2.093   1.0151e-01
   1_occ:  14.013  0.176  0.424 85.019  0.036  2.093   1.0151e-01
   2_bss:  14.013  0.176  0.424 85.019  0.036  2.093   1.0151e-01
   2_xyz:   8.099  0.075  0.298 82.769  0.029  2.170   5.8854e-02
   2_adp:   8.099  0.075  0.298 82.769  0.029  2.170   5.8854e-02
   2_occ:   8.099  0.075  0.298 82.769  0.029  2.170   5.8854e-02
   3_bss:   8.099  0.075  0.298 82.769  0.029  2.170   5.8854e-02
   3_xyz:   8.180  0.084  0.368 86.507  0.033  2.160   8.6271e-02
   3_adp:   8.180  0.084  0.368 86.507  0.033  2.160   8.6271e-02
   3_occ:   8.180  0.084  0.368 86.507  0.033  2.160   8.6271e-02
   4_bss:   8.180  0.084  0.368 86.507  0.033  2.160   8.6271e-02
   4_xyz:   8.209  0.057  0.248 82.577  0.046  2.215   6.2114e-02
   4_adp:   8.209  0.057  0.248 82.577  0.046  2.215   6.2114e-02
   4_occ:   8.209  0.057  0.248 82.577  0.046  2.215   6.2114e-02
   5_bss:   8.209  0.057  0.248 82.577  0.046  2.215   6.2114e-02
   5_xyz:   6.283  0.050  0.226 82.283  0.040  2.328   4.6931e-02
   5_adp:   6.283  0.050  0.226 82.283  0.040  2.328   4.6931e-02
   5_occ:   6.283  0.050  0.226 82.283  0.040  2.328   4.6931e-02
   5_bss:   6.283  0.050  0.226 82.283  0.040  2.328   4.6931e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  78.02   0.00  15.47  69.75   0.00  13.81  78.02   0.00  24.51
   1_occ:  78.02   0.00  15.47  69.75   0.00  13.81  78.02   0.00  24.51
   2_bss:  78.02   0.00  15.47  69.75   0.00  13.81  78.02   0.00  24.51
   2_xyz:  78.02   0.00  15.47  69.75   0.00  13.81  78.02   0.00  24.51
   2_adp:  88.48   0.00  14.82  64.34   0.00  12.09  88.48   0.00  29.70
   2_occ:  88.48   0.00  14.82  64.34   0.00  12.09  88.48   0.00  29.70
   3_bss:  88.48   0.00  14.82  64.34   0.00  12.09  88.48   0.00  29.70
   3_xyz:  88.48   0.00  14.82  64.34   0.00  12.09  88.48   0.00  29.70
   3_adp: 112.65   0.00  14.29 112.65   0.00  10.47  89.09   1.46  35.07
   3_occ: 112.65   0.00  14.29 112.65   0.00  10.47  89.09   1.46  35.07
   4_bss: 112.65   0.00  14.29 112.65   0.00  10.47  89.09   1.46  35.07
   4_xyz: 112.65   0.00  14.29 112.65   0.00  10.47  89.09   1.46  35.07
   4_adp: 100.45   0.00  15.40  92.49   0.00  10.26 100.45   2.83  43.36
   4_occ: 100.45   0.00  15.40  92.49   0.00  10.26 100.45   2.83  43.36
   5_bss: 100.45   0.00  15.40  92.49   0.00  10.26 100.45   2.83  43.36
   5_xyz: 100.45   0.00  15.40  92.49   0.00  10.26 100.45   2.83  43.36
   5_adp:  94.72   0.00  14.48  93.64   0.00   9.79  94.72   3.18  40.01
   5_occ:  94.72   0.00  14.48  93.64   0.00   9.79  94.72   3.18  40.01
   5_bss:  96.05   1.33  15.81  94.97   1.33  11.12  96.05   4.51  41.34
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.294    0.017    0.411
   1_adp:    1.294    0.017    0.411
   1_occ:    1.294    0.017    0.411
   2_bss:    1.294    0.017    0.411
   2_xyz:    1.867    0.016    0.565
   2_adp:    1.867    0.016    0.565
   2_occ:    1.867    0.016    0.565
   3_bss:    1.867    0.016    0.565
   3_xyz:    1.683    0.050    0.724
   3_adp:    1.683    0.050    0.724
   3_occ:    1.683    0.050    0.724
   4_bss:    1.683    0.050    0.724
   4_xyz:    1.697    0.063    0.783
   4_adp:    1.697    0.063    0.783
   4_occ:    1.697    0.063    0.783
   5_bss:    1.697    0.063    0.783
   5_xyz:    1.742    0.063    0.812
   5_adp:    1.742    0.063    0.812
   5_occ:    1.742    0.063    0.812
   5_bss:    1.742    0.063    0.812
------------------------------------------------------------------------

CPU time actual refinement: 357.38


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_395/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/trial/run_395/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_395/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_395/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_395/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 357.23 
  Macro-tasks:
    bulk solvent and scale       = 40.32  
    individual site refinement   = 154.54 
    weights calculation          = 32.80  
    collect and process          = 6.27   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 234.04 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 113.92 
    alpha_beta                      = 7.82   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 125.27 
    fmodel                         = 7.50   
    r_factors                      = 0.22   
    phase_errors                   = 9.97   
    foms                           = 0.29   
    TOTAL for micro-tasks          = 268.58 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.933 micro seconds
Total CPU time: 6.18 minutes
from_scatterers_fft:    679 calls, 113.62 s
gradients_fft:          624 calls, 111.21 s

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

# Date 2008-01-16 Time 01:28:29 PST -0800 (1200475709.42 s)
Start R-work = 0.5029, R-free = 0.4903 (no bulk solvent and anisotropic scale)
Final R-work = 0.1458, R-free = 0.1924 (no bulk solvent and anisotropic scale)

Start R-work = 0.4941, R-free = 0.4786
Final R-work = 0.1281, R-free = 0.1761